Open Science

Hello! Is this thing on? The last 12 months have seen significant life changes (seemingly successful) for many of the people within and around the OWW community. Because OWW is a community (of researchers) we are past due for an update on how we are doing and open discussions of where we might want to be heading.

First, a few of the changes:

All of the founding researchers who created and obtained funding in support of OWW managed to earn their PhDs from MIT. Many of these folks have successfully launched a new company, Ginkgo BioWorks, in order to help make biology easy to engineer. Indeed!

Lorrie LeJeune, who was our Managing Director was lured away to become a Senior Editor at Nature Education, which is an incredible opportunity for her to impact the lives of many learners. Good luck Lorrie!

The Endy Lab wound down at MIT and has been reborn at Stanford. Personally, I’ve moved twice, sold one condo, bought one house, helped to design and manage the construction of a new laboratory, and have been assembling a new research team. Phew.

Second, what’s not changed:

Bill Flanagan remains gainfully employed at MIT, working to make OWW better and helping to put out the fires that flare up. Simply put, Bill is an incredible resource for OWW and we are ridiculously lucky to have somebody at his skill level and with his strategic perspective at the heart of OWW.

We currently maintain funding from the US National Science Foundation in support of OWW. To clarify one point in the recent and fantastic article by Jakob Sukale, the NSF grant expires 30 April 2010. This grant currently pays for Bill’s salary and our server costs. We are currently underspending on this grant and I will likely ask for a no-cost extension which, if granted, could extend our existing funding runway to April 2011.

Third, who is OWW?

I’ve found it very useful to understand who is actually using OWW. I’d suspected that some people tend to talk about OWW and openness in research but that fewer folks are actually living the dream, so to speak. Well, turns out that thanks to Bill, OWW maintains a statistics page here. There are ~6000 registered OWW users (roughly doubling over the past year). About 50 different users make edits to OWW pages on any given day. About 500 unique users make edits each month. Over 100,000 unique visitors browse OWW each month. This is incredible!

From a different perspective, OWW is incredibly small. We also represent a broader experiment in changing the process of research that is very much in a fragile intermediate stage of its development. Michael Nielsen did a good job of capturing some of the issues in his recent article, “Doing Science in the Open.” Stated differently and from a personal perspective, I would currently be hard pressed to make a successful argument that supporting and using OWW has made the research in my own laboratory significantly better, as judged by our traditionally published results. On the one hand, we had a great experience using OWW as a platform for developing a shared reference standard for measuring promoter activity in vivo. On the other hand, using OWW as it exists today has led to increased frustration with the slow inanities to be found within the conventional research publication process, while simultaneously and naively reducing the pressure to publish more formally and enabling others outside the (v. small) OWW community to “borrow” results without giving credit. Perhaps this shouldn’t be surprising. All said, I’m more invested in OWW than ever before, and am convinced that we are figuring out a new way to do research. We just have a lot of work to do in order to make the transition complete.

So fourth, what’s happening in terms of thinking about where we might go?

Lorrie LeJeune and Jason Kelly did a tremendous job exploring the entire process of research, from brainstorming ideas to promulgating results. Some of these ideas are summarized here. Many interesting questions and debates arise from considering this framing. For example, is OWW about the information and knowledge maintained on our servers, or is it about the community of researchers that produces this content? (personally, I think that the answer is both). Stated differently, should OWW support the process of research or should we focus on the capture and promulgation of research results? (again, I’d vote both). As a different example, does OWW exist primarily in order to stand as a shining beacon of openness in research, or are we simply trying to make the research process better which, given today’s information and communication technology platforms, tends to select for doing many more things in the open? (more on this third example below).

Bill Flanagan and I have been churning through the exciting opportunities that seem to continuously emerge given ongoing advances in information and communication technologies. Some people refer to OWW as a wiki. This makes me cringe. Wikis are great but we likely need to transcend this framing in order to best realize solutions that could be developed in service of our community and our work. You can find many early examples of this, such as Bill’s pilot efforts to integrate OWW with online document systems (e.g., Google Docs).

So, where should we go? My own sense is that we should go meta and support the integration of many web-based tools and communities in support of making the research process better. We will end up doing many more things in the open as a result. We also need to partner more effectively with existing modes and channels of peer review and recognition. But this is just my sense, so please chime in with your two cents, either via our Google discussion group, in the comments below, or by editing the appropriate OWW page. We need to hear from the people who are depending on OWW, or who would use OWW if <blank> happened. Also, for those of us for whom OWW is an essential part of our research existence, please participate in discussions about how to best guarantee the future funding of our operation. We have time to work through different models, but need to start doing so now. Our Discussion list is
just a click away.

Those in the open access movement had watched BioMed Central with keen interest. Founded in 2000, it was the first for-profit open access publisher and advocates feared that when the company was sold, its approach might change. But Cockerill assured editors that a BMC board of trustees “will continue to safeguard BioMed Central’s open access policy in the future.” Springer “has been notable…for its willingness to experiment with open access publishing,” Cockerill said in a release circulated with the email to editors.

No information yet as to how much this acquisition cost.

What do you think about this? Will Springer just “experiment” with open access publishing for a while and then close the gates? Or is this a genuine attempt to join the OA movement?

The main issue is the fear of rivals stealing data. The second one is: will I be able to publish? And that depends on the publisher. Most publishers regard what we do as the equivalent of presenting at a conference, or a preprint. That hasn’t been tested across a wide range of publishers, and there’s at least one — the American Chemical Society — that doesn’t allow prepublication in any form whatsoever. There’s also a legitimate concern that a lot of people will put out a lot of rubbish.

And JC Bradley’s view of an open notebook:

The basic philosophy of open-notebook science is to have no insider information. Essentially all the information that is available to the [research] group is available to the rest of the world. You have an objective, a procedure and a log section, in which you report what you actually do.

These is far more to be said about sharing data and the use of open notebooks. Both Cameron and JC Bradley have written about their experiences on their blogs. I’d recommend snooping around because there is much to read.

The Boston Globe has recently published an article showcasing a few projects that belong to what they refer to as “a peaceful insurgency in science”, an open-science movement per se.

Barry Canton, Ph.D. graduate at MIT and co-founder of OpenWetWare, is portrayed as an example of this movement. By posting his work on OWW (and also to an established journal!), his work has been incorporated into 18 different projects in other labs.

One recent SciFoo related post that caught my eye was Mario Pineda-Krch’s thoughts on the idea of distributed open notebook science. Yes, distributed.

As Mario mentions, by using a client based wiki setup like Tiddlywiki, the user has more flexibility by not having to rely on network access. Furthermore, a version control system like Git brings redundancy allowing anyone to download the latest version of the notebook. The wiki + the data with full control.

The idea of open notebook science is not necessarily a new one. The term was coined by JC Bradley roughly two years ago. However, it’s been tough to go mainstream due to the fact that notebooks are usually foreseen to be private, thus failing in the “open” department. However, this hasn’t stopped many from setting up lab notebooks online like Jean-Claude Bradley, Garrett Lisi or any of the dozens of OpenWetWare lab notebook users.

Just a few days ago, an article by Declan Butler was published in Nature regarding PLoS‘ open-access publishing model. This article was not well accepted by various open access advocates and science bloggers in general.

What I find to be the most notorious aspect in this whole string of events is that there is quite a large community of science bloggers that are ready to offer their “peer-review” in situations such as these. Is this a good thing? I would like to believe so…

If we try and apply ANYTHING other than the public domain to scientific facts we shall no be able to manage scientific data. Problems include aggregation, restrictions (however reasonable) on re-use, cascading attribution, different jurisdictions.